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- PDB-6odl: Crystal structure of GluN2A agonist binding domain with 4-butyl-(... -

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Basic information

Entry
Database: PDB / ID: 6odl
TitleCrystal structure of GluN2A agonist binding domain with 4-butyl-(S)-CCG-IV
ComponentsGlutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
KeywordsTRANSPORT PROTEIN / NMDA RECEPTOR / ANTAGONIST / RECEPTOR
Function / homology
Function and homology information


mesencephalic trigeminal nucleus development / regulation of response to alcohol / response to ammonium ion / response to environmental enrichment / neurotransmitter receptor transport, plasma membrane to endosome / directional locomotion / receptor recycling / auditory behavior / Assembly and cell surface presentation of NMDA receptors / response to carbohydrate ...mesencephalic trigeminal nucleus development / regulation of response to alcohol / response to ammonium ion / response to environmental enrichment / neurotransmitter receptor transport, plasma membrane to endosome / directional locomotion / receptor recycling / auditory behavior / Assembly and cell surface presentation of NMDA receptors / response to carbohydrate / protein localization to postsynaptic membrane / cellular response to magnesium ion / sleep / serotonin metabolic process / positive regulation of mitochondrial calcium ion concentration / response to hydrogen sulfide / response to other organism / response to methylmercury / regulation of ARF protein signal transduction / locomotion / response to manganese ion / response to glycoside / cellular response to dsRNA / cellular response to lipid / dendritic spine organization / positive regulation of inhibitory postsynaptic potential / regulation of NMDA receptor activity / response to amine / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / cellular response to zinc ion / NMDA selective glutamate receptor complex / spinal cord development / glutamate binding / startle response / voltage-gated monoatomic cation channel activity / calcium ion transmembrane import into cytosol / dopamine metabolic process / glutamate receptor signaling pathway / response to lithium ion / parallel fiber to Purkinje cell synapse / associative learning / regulation of neuronal synaptic plasticity / response to light stimulus / regulation of postsynaptic membrane potential / multicellular organismal response to stress / action potential / modulation of excitatory postsynaptic potential / monoatomic cation transmembrane transport / positive regulation of protein targeting to membrane / cellular response to glycine / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / neurogenesis / conditioned place preference / regulation of long-term neuronal synaptic plasticity / postsynaptic density, intracellular component / response to fungicide / monoatomic cation channel activity / sensory perception of pain / cellular response to manganese ion / glutamate-gated receptor activity / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / visual learning / cell adhesion molecule binding / learning / ionotropic glutamate receptor signaling pathway / hippocampus development / protein tyrosine kinase binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cellular response to amino acid stimulus / excitatory postsynaptic potential / dendrite membrane / positive regulation of excitatory postsynaptic potential / cytoplasmic vesicle membrane / response to cocaine / response to nicotine / sodium ion transmembrane transport / synaptic membrane / response to wounding / negative regulation of protein catabolic process / synaptic transmission, glutamatergic / memory / long-term synaptic potentiation / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / regulation of synaptic plasticity / regulation of membrane potential / response to calcium ion / cellular response to growth factor stimulus / response to lead ion / postsynaptic density membrane / modulation of chemical synaptic transmission / calcium channel activity / calcium ion transport / calcium ion transmembrane transport / calcium-dependent protein binding
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Chem-M7V / Glutamate receptor / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMou, T.C. / Clausen, R.P. / Sprang, S.R. / Hansen, K.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R01NS097536 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Stereoselective synthesis of novel 2'-(S)-CCG-IV analogues as potent NMDA receptor agonists.
Authors: Maolanon, A. / Papangelis, A. / Kawiecki, D. / Mou, T.C. / Syrenne, J.T. / Yi, F. / Hansen, K.B. / Clausen, R.P.
History
DepositionMar 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
B: Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1384
Polymers62,7082
Non-polymers4302
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-14 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.094, 52.094, 197.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Mass: 31353.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q00959, UniProt: G3V9C5
#2: Chemical ChemComp-M7V / (1S,2R)-2-[(S)-amino(carboxy)methyl]-1-butylcyclopropane-1-carboxylic acid


Mass: 215.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M AMMONIUM SULFATE AND 16-22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.27→30 Å / Num. obs: 22638 / % possible obs: 94.2 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rpim(I) all: 0.052 / Rrim(I) all: 0.125 / Net I/σ(I): 12
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.75 / Num. unique obs: 2296 / CC1/2: 0.596 / Rpim(I) all: 0.233 / Rrim(I) all: 0.482 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A5S

2a5s


Resolution: 2.3→19.026 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 29.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2827 1915 8.75 %
Rwork0.2243 --
obs0.2294 21886 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4420 0 0 170 4590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034522
X-RAY DIFFRACTIONf_angle_d0.766124
X-RAY DIFFRACTIONf_dihedral_angle_d7.4923207
X-RAY DIFFRACTIONf_chiral_restr0.247688
X-RAY DIFFRACTIONf_plane_restr0.003782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.35770.38191420.28891497X-RAY DIFFRACTION99
2.3577-2.42130.31471410.26151486X-RAY DIFFRACTION99
2.4213-2.49240.32131470.25051506X-RAY DIFFRACTION99
2.4924-2.57270.28671480.24431510X-RAY DIFFRACTION100
2.5727-2.66440.36351320.26081394X-RAY DIFFRACTION93
2.6644-2.77080.31941360.29491414X-RAY DIFFRACTION93
2.7708-2.89640.35261440.25681523X-RAY DIFFRACTION100
2.8964-3.04860.32291420.25451494X-RAY DIFFRACTION100
3.0486-3.23870.31971360.23251530X-RAY DIFFRACTION99
3.2387-3.48730.27251130.25471165X-RAY DIFFRACTION77
3.4873-3.83570.34331160.24681207X-RAY DIFFRACTION80
3.8357-4.38480.23931220.20291210X-RAY DIFFRACTION80
4.3848-5.50210.23911440.16741513X-RAY DIFFRACTION100
5.5021-19.02660.18831520.16681522X-RAY DIFFRACTION99

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